Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 2 of 129
Found at i:219926 original size:20 final size:20
Alignment explanation
Indices: 219901--219952 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
219891 AACAAACTAG
*
219901 ATGCCATGCACTAATTGACA
1 ATGCCATGCACTAACTGACA
* *
219921 ATGCCATGTACTAACTGACT
1 ATGCCATGCACTAACTGACA
*
219941 GTGCCATGCACT
1 ATGCCATGCACT
219953 TGTGCTAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (20 bp):
ATGCCATGCACTAACTGACA
Found at i:220560 original size:45 final size:45
Alignment explanation
Indices: 220496--220584 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
220486 GAGCCTGGCC
* *
220496 TTTCTAGAACCTTCGATGCCCATACACCTGGCCTACCTCTAGGTT
1 TTTCTAGAACCTTCCATGCCCACACACCTGGCCTACCTCTAGGTT
* * *
220541 TTTCTAGAGA-CTTCCATGCCCGCACACTTGGCCTATCTCTAGGT
1 TTTCTAGA-ACCTTCCATGCCCACACACCTGGCCTACCTCTAGGT
220585 GGTTCTAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.31
Consensus pattern (45 bp):
TTTCTAGAACCTTCCATGCCCACACACCTGGCCTACCTCTAGGTT
Found at i:224168 original size:12 final size:12
Alignment explanation
Indices: 224147--224183 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
224137 TTCATTGGGG
224147 AATA-AAGGGCC
1 AATATAAGGGCC
224158 AATATAAGGGCC
1 AATATAAGGGCC
224170 AATATAAGGGCC
1 AATATAAGGGCC
224182 AA
1 AA
224184 CGACTAGCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (12 bp):
AATATAAGGGCC
Found at i:224452 original size:23 final size:23
Alignment explanation
Indices: 224413--224461 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
224403 AGATGGTGCA
*
224413 GCACATGCTGACGGATAAAGCAG
1 GCACATGCTGACAGATAAAGCAG
* * *
224436 GCACATGCTGGCAGATAGAGCGG
1 GCACATGCTGACAGATAAAGCAG
224459 GCA
1 GCA
224462 TATGTCTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.22, G:0.35, T:0.12
Consensus pattern (23 bp):
GCACATGCTGACAGATAAAGCAG
Found at i:224525 original size:45 final size:45
Alignment explanation
Indices: 224471--224606 Score: 173
Period size: 45 Copynumber: 3.0 Consensus size: 45
224461 ATATGTCTTA
* * *
224471 ACCATCATCAGCACAAGTTGGCCTTTGGTATAAGCACTTGCCTTG
1 ACCACCATCAGCATAAGTTGGCCCTTGGTATAAGCACTTGCCTTG
* * * **
224516 ACCACCATCAACATAAGTTGGCCCTTGGTATAGGCACTTACCTCA
1 ACCACCATCAGCATAAGTTGGCCCTTGGTATAAGCACTTGCCTTG
* * *
224561 ACCACCATCAGCATATGTTGGCCCTTGGTGTAAGCACATGCCTTG
1 ACCACCATCAGCATAAGTTGGCCCTTGGTATAAGCACTTGCCTTG
224606 A
1 A
224607 TCAGCATTGG
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (45 bp):
ACCACCATCAGCATAAGTTGGCCCTTGGTATAAGCACTTGCCTTG
Found at i:234095 original size:10 final size:10
Alignment explanation
Indices: 234080--234109 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
234070 ATTGACATTT
234080 TATATTTTAA
1 TATATTTTAA
234090 TATATTTTAA
1 TATATTTTAA
234100 T-TATTTTAA
1 TATATTTTAA
234109 T
1 T
234110 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:234106 original size:9 final size:9
Alignment explanation
Indices: 234082--234111 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
234072 TGACATTTTA
234082 TATTTTAAT
1 TATTTTAAT
234091 ATATTTTAAT
1 -TATTTTAAT
234101 TATTTTAAT
1 TATTTTAAT
234110 TA
1 TA
234112 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:244892 original size:48 final size:48
Alignment explanation
Indices: 244786--244892 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
244776 GAATAGTGGC
* * *
244786 AGGTACTATAGCACCCAAACAAGGAAGGCTCTATAAGGCCTTAACTTT
1 AGGTACTATAGCACCCAAACAAGGAAGACTCTATAAAGCCCTAACTTT
* * *
244834 AGGTATTATAGCACCCAAATGAA-GAAGACTCTGA-AAAGCCCTAGCTTT
1 AGGTACTATAGCACCCAAA-CAAGGAAGACTCT-ATAAAGCCCTAACTTT
*
244882 GGGTACTATAG
1 AGGTACTATAG
244893 TGTCCAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
48 46 0.94
49 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (48 bp):
AGGTACTATAGCACCCAAACAAGGAAGACTCTATAAAGCCCTAACTTT
Found at i:255061 original size:44 final size:45
Alignment explanation
Indices: 255013--255112 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 45
255003 CATCATCGTT
* * **
255013 ACAAGCTAGCTTTTGGTACAGATACTTGCCT-AACCACCATTGGC
1 ACAAGCTAGCCTTTGGTACAGACACTTGCCTCAACCACCATCAGC
* * *
255057 ACAAGCTGGCCTTTGGTACGGGCACTTGCCTCAACCACCATCAGC
1 ACAAGCTAGCCTTTGGTACAGACACTTGCCTCAACCACCATCAGC
*
255102 ACATGCTAGCC
1 ACAAGCTAGCC
255113 CATGATATAG
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 26 0.57
45 20 0.43
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (45 bp):
ACAAGCTAGCCTTTGGTACAGACACTTGCCTCAACCACCATCAGC
Found at i:262969 original size:6 final size:7
Alignment explanation
Indices: 262927--262987 Score: 59
Period size: 7 Copynumber: 8.1 Consensus size: 7
262917 TTTGGTAATT
262927 TTTTTTA
1 TTTTTTA
262934 TTAATTTTA
1 TT--TTTTA
* *
262943 TTATTAA
1 TTTTTTA
262950 TTATTATTA
1 TT-TT-TTA
262959 TTTTTTA
1 TTTTTTA
262966 TTTTTTA
1 TTTTTTA
262973 TTTTTTA
1 TTTTTTA
*
262980 ATTTTTA
1 TTTTTTA
262987 T
1 T
262988 GGCTAACAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 30 0.68
8 3 0.07
9 11 0.25
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTTA
Found at i:262984 original size:13 final size:14
Alignment explanation
Indices: 262922--262984 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 14
262912 ATTTTTTTGG
262922 TAATTTT-TTTTAT
1 TAATTTTATTTTAT
262935 TAATTTTATTATTAAT
1 TAATTTTATT-TT-AT
262951 T-ATTATTATTTT-T
1 TAATT-TTATTTTAT
*
262964 TATTTTTTATTTT-T
1 TA-ATTTTATTTTAT
262978 TAATTTT
1 TAATTTT
262985 TATGGCTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
13 13 0.31
14 12 0.29
15 9 0.21
16 8 0.19
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TAATTTTATTTTAT
Found at i:263265 original size:9 final size:8
Alignment explanation
Indices: 263248--263287 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
263238 TAAAACCCAA
263248 TTTTTTTG
1 TTTTTTTG
263256 TTTTTATTG
1 TTTTT-TTG
263265 TTTTCTTT-
1 TTTT-TTTG
263273 TTTTTTTG
1 TTTTTTTG
263281 TTTTTTT
1 TTTTTTT
263288 TTGTCAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 3 0.10
8 16 0.55
9 9 0.31
10 1 0.03
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:263288 original size:9 final size:9
Alignment explanation
Indices: 263248--263288 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
263238 TAAAACCCAA
263248 TTTTTTTGT
1 TTTTTTTGT
*
263257 TTTTATTG-
1 TTTTTTTGT
*
263265 TTTTCTT-T
1 TTTTTTTGT
263273 TTTTTTTGT
1 TTTTTTTGT
263282 TTTTTTT
1 TTTTTTT
263289 TGTCAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.88
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:263386 original size:34 final size:36
Alignment explanation
Indices: 263312--263397 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 36
263302 AACAAGACCG
** *
263312 GGACAACACTGTAAGTCAAAAAATAAGTAACGATTG
1 GGACAACACCATAAGTCAAAAAATAAGTAACGATTA
**
263348 GGAC-A-ACCATAAGTCAAAAAATAAAG-AATTATTA
1 GGACAACACCATAAGTCAAAAAAT-AAGTAACGATTA
263382 GGACAACACCATAAGT
1 GGACAACACCATAAGT
263398 TGAAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
34 24 0.57
35 5 0.12
36 13 0.31
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (36 bp):
GGACAACACCATAAGTCAAAAAATAAGTAACGATTA
Found at i:263804 original size:33 final size:33
Alignment explanation
Indices: 263742--263982 Score: 163
Period size: 33 Copynumber: 7.2 Consensus size: 33
263732 TTAAATTGGA
* * * *
263742 CTTAAATCTTTTCATGATGTGCTAGCCAAACTGGG
1 CTTAAAT-TTTTCATTA-ATGCTAGCTAAACTAGG
* *
263777 CTTAAATTTTTCATTAATGCCAGCCAAACTAGG
1 CTTAAATTTTTCATTAATGCTAGCTAAACTAGG
* ** *
263810 CTTAAATCTTTCATTGTTGTTAG-TCAAACTAGG
1 CTTAAATTTTTCATTAATGCTAGCT-AAACTAGG
*
263843 CTTAAATCTTTTCATAAAGTGCTAGCTAAAC-AGGG
1 CTTAAAT-TTTTCATTAA-TGCTAGCTAAACTA-GG
* *
263878 CTTAAATTTTT-ATTGGA-GCCAGCTAAACTAGG
1 CTTAAATTTTTCATT-AATGCTAGCTAAACTAGG
* * * * * *
263910 CTTAAATCTTTCCATGAGGTGCTAGATAAATTGGG
1 CTTAAAT-TTTTCATTA-ATGCTAGCTAAACTAGG
*
263945 CTT-AA-TTTTCATTGATG-TCAGCTAAACTAGG
1 CTTAAATTTTTCATTAATGCT-AGCTAAACTAGG
263976 CTTAAAT
1 CTTAAAT
263983 CCTTTCATGA
Statistics
Matches: 159, Mismatches: 33, Indels: 30
0.72 0.15 0.14
Matches are distributed among these distances:
30 1 0.01
31 14 0.09
32 27 0.17
33 53 0.33
34 24 0.15
35 39 0.25
36 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (33 bp):
CTTAAATTTTTCATTAATGCTAGCTAAACTAGG
Found at i:263820 original size:68 final size:69
Alignment explanation
Indices: 263742--264057 Score: 196
Period size: 67 Copynumber: 4.7 Consensus size: 69
263732 TTAAATTGGA
* *
263742 CTTAAATCTTTTCA-TGATGTGCTAGCCAAACTGGGCTTAAAT-TTTTCATTAA-TGCCAGCCAA
1 CTTAAATCTTTTCATTG-T-TGCTAGCCAAACTAGGCTTAAATCTTTTCATAAAGTGCCAGCCAA
263804 ACTA-GG
64 AC-AGGG
* * * *
263810 CTTAAATC-TTTCATTGTTGTTAGTCAAACTAGGCTTAAATCTTTTCATAAAGTGCTAGCTAAAC
1 CTTAAATCTTTTCATTGTTGCTAGCCAAACTAGGCTTAAATCTTTTCATAAAGTGCCAGCCAAAC
263874 AGGG
66 AGGG
** * * * * * * ** *
263878 CTTAAAT-TTTT-ATTGGAGCCAGCTAAACTAGGCTTAAATCTTTCCATGAGGTGCTAGATAAAT
1 CTTAAATCTTTTCATTGTTGCTAGCCAAACTAGGCTTAAATCTTTTCATAAAGTGCCAGCCAAAC
*
263941 TGGG
66 AGGG
* * * * **
263945 CTT-AA--TTTTCATTGATG-TCAGCTAAACTAGGCTTAAATCCTTTCAT-GAG-GACCAGGTAA
1 CTTAAATCTTTTCATTGTTGCT-AGCCAAACTAGGCTTAAATCTTTTCATAAAGTG-CCAGCCAA
***
264004 TTTGGG
64 ACAGGG
* *
264010 CTTAAATC-TTT-ATTGGGTGCTAGCC-AACTTGGGCTTAAATCTTTTCAT
1 CTTAAATCTTTTCATT-GTTGCTAGCCAAAC-TAGGCTTAAATCTTTTCAT
264058 GAGATGCTAG
Statistics
Matches: 202, Mismatches: 32, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
64 1 0.00
65 19 0.09
66 60 0.30
67 89 0.44
68 33 0.16
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.36
Consensus pattern (69 bp):
CTTAAATCTTTTCATTGTTGCTAGCCAAACTAGGCTTAAATCTTTTCATAAAGTGCCAGCCAAAC
AGGG
Found at i:263972 original size:133 final size:133
Alignment explanation
Indices: 263802--264119 Score: 356
Period size: 133 Copynumber: 2.4 Consensus size: 133
263792 AATGCCAGCC
* * *
263802 AAACTAGGCTTAAATCTTTCATTGTTGTTAG-TCAAACTAGGCTTAAATCTTTTCATAAAGTG-C
1 AAACTGGGCTT-AAT-TTTCATTGATGTCAGCT-AAACTAGGCTTAAATCTTTTCAT-AAG-GAC
* *
263865 TAGCTAAACAGGGCTTAAATTTTTATT-GGAGCCAGCTAAAC-TAGGCTTAAATCTTTCCATGAG
61 CAGCTAAACAGGGCTTAAATCTTTATTGGGAGCCAGC-AAACTTAGGCTTAAATCTTTCCATGAG
*
263928 GTGCTAGAT
125 ATGCTAGAT
* * * *
263937 AAATTGGGCTTAATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCCTTTCATGAGGACCAGGT
1 AAACTGGGCTTAATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCTTTTCATAAGGACCAGCT
*** * * * * *
264002 AATTTGGGCTTAAATCTTTATTGGGTGCTAGCCAACTTGGGCTTAAATCTTTTCATGAGATGCTA
66 AAACAGGGCTTAAATCTTTATTGGGAGCCAGCAAACTTAGGCTTAAATCTTTCCATGAGATGCTA
264067 GAT
131 GAT
* * * *
264070 AAACTGTGCTTAATTTTCATTGGTGCCAGCTAAACTAGGCTTAAAACTTT
1 AAACTGGGCTTAATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCTTT
264120 GTTAGGCTAG
Statistics
Matches: 155, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
131 1 0.01
132 27 0.17
133 114 0.74
134 4 0.03
135 9 0.06
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (133 bp):
AAACTGGGCTTAATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCTTTTCATAAGGACCAGCT
AAACAGGGCTTAAATCTTTATTGGGAGCCAGCAAACTTAGGCTTAAATCTTTCCATGAGATGCTA
GAT
Found at i:263992 original size:66 final size:67
Alignment explanation
Indices: 263802--264114 Score: 275
Period size: 67 Copynumber: 4.7 Consensus size: 67
263792 AATGCCAGCC
* * * * * *
263802 AAACTAGGCTTAAATCTTTCATTGTTGTTAG-TCAAACTAGGCTTAAATCTTTTCATAAAGTGCT
1 AAACTGGGCTTAAAT-TTTCATTGATGTCAGCT-AAACTAGGCTTAAATCCTTTCATGAGGTGCT
*
263866 AGCT
64 AGAT
* * *
263870 AAACAGGGCTTAAATTTTTATTGGA-GCCAGCTAAACTAGGCTTAAAT-CTTTCCATGAGGTGCT
1 AAACTGGGCTTAAATTTTCATT-GATGTCAGCTAAACTAGGCTTAAATCCTTT-CATGAGGTGCT
263933 AGAT
64 AGAT
* * *
263937 AAATTGGGCTT-AATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCCTTTCATGAGG-ACCAG
1 AAACTGGGCTTAAATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCCTTTCATGAGGTGCTAG
*
264000 GT
66 AT
** * * * * *
264002 AATTTGGGCTTAAATCTTT-ATTG-GGTGCTAGC-CAACTTGGGCTTAAATCTTTTCATGAGATG
1 AAACTGGGCTTAAAT-TTTCATTGATGT-C-AGCTAAAC-TAGGCTTAAATCCTTTCATGAGGTG
264064 CTAGAT
62 CTAGAT
* * *
264070 AAACTGTGCTT-AATTTTCATTGGTGCCAGCTAAACTAGGCTTAAA
1 AAACTGGGCTTAAATTTTCATTGATGTCAGCTAAACTAGGCTTAAA
264115 ACTTTGTTAG
Statistics
Matches: 198, Mismatches: 33, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
65 18 0.09
66 66 0.33
67 86 0.43
68 28 0.14
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (67 bp):
AAACTGGGCTTAAATTTTCATTGATGTCAGCTAAACTAGGCTTAAATCCTTTCATGAGGTGCTAG
AT
Found at i:264205 original size:34 final size:33
Alignment explanation
Indices: 264158--264241 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 33
264148 GAGTGCCAAC
*
264158 TAATCTGGACTTAAATTTTTTCATGAGGGCCAGG
1 TAATCTGGGCTTAAATTTTTTCAT-AGGGCCAGG
** * *
264192 TAATCTGGGCTTAAA--ACTTCATTGGGCTAGG
1 TAATCTGGGCTTAAATTTTTTCATAGGGCCAGG
*
264223 TAATTTGGGCTTAAATTTT
1 TAATCTGGGCTTAAATTTT
264242 CTTTAGATGC
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
31 21 0.52
32 5 0.12
34 14 0.35
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (33 bp):
TAATCTGGGCTTAAATTTTTTCATAGGGCCAGG
Found at i:264334 original size:33 final size:33
Alignment explanation
Indices: 264230--264347 Score: 116
Period size: 34 Copynumber: 3.5 Consensus size: 33
264220 AGGTAATTTG
* * *
264230 GGCTTAAA-TTTTCTTTAGATGCCAACC-AACTT
1 GGCTTAAATTTTTCATT-GATGGCAGCCAAACTT
* *
264262 GGACTTAAAATTTTTCATT-AAGTGCTAGCTAAACTT
1 GG-CTT-AAATTTTTCATTGATG-GC-AGCCAAACTT
264298 GGCTTAAATTTTTCATTGATGGCAGCCAAACTT
1 GGCTTAAATTTTTCATTGATGGCAGCCAAACTT
264331 GGCTTAAATCTTTTCAT
1 GGCTTAAAT-TTTTCAT
264348 GAGATGCCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
32 2 0.03
33 23 0.32
34 25 0.35
35 14 0.20
36 7 0.10
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (33 bp):
GGCTTAAATTTTTCATTGATGGCAGCCAAACTT
Found at i:264394 original size:29 final size:29
Alignment explanation
Indices: 264360--264422 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
264350 GATGCCAAAT
264360 AAACTAAGCTTAAAACCT-AGGTGCCAGCA
1 AAACTAAGCTTAAAACCTGA-GTGCCAGCA
* * *
264389 AAACTAGGCTTAAATCCTGAGTGCCAGCT
1 AAACTAAGCTTAAAACCTGAGTGCCAGCA
264418 AAACT
1 AAACT
264423 GGAATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (29 bp):
AAACTAAGCTTAAAACCTGAGTGCCAGCA
Found at i:264499 original size:33 final size:35
Alignment explanation
Indices: 264414--264504 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 35
264404 CCTGAGTGCC
* *
264414 AGCTAAACTGGAATTAAATCTTTTCATGGGGTGTT
1 AGCTAAACTGGAATTAAATCTTTTCATGGGATGCT
* ** * *
264449 AGATAAACTGGGCTTAAATCTTTT-GT-TGATGCT
1 AGCTAAACTGGAATTAAATCTTTTCATGGGATGCT
*
264482 AGCTAAACTGGATTTAAATCTTT
1 AGCTAAACTGGAATTAAATCTTT
264505 ATTAGTGTCA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
33 24 0.52
34 1 0.02
35 21 0.46
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (35 bp):
AGCTAAACTGGAATTAAATCTTTTCATGGGATGCT
Found at i:265556 original size:29 final size:32
Alignment explanation
Indices: 265524--265594 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
265514 CACCGATTCA
265524 TTTCTTTCATTC-TC-TT-TTTTTTTCCTTAT-
1 TTTCTTTCATTCTTCTTTCTTTTTTTCCTT-TC
**
265553 TTTCTTTTGTTCTTCTTTCTTTTTTTCCTTTC
1 TTTCTTTCATTCTTCTTTCTTTTTTTCCTTTC
265585 TTT-TTTCATT
1 TTTCTTTCATT
265595 TTACTCTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 10 0.29
30 2 0.06
31 8 0.24
32 14 0.41
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTCTTTCATTCTTCTTTCTTTTTTTCCTTTC
Found at i:265585 original size:13 final size:14
Alignment explanation
Indices: 265553--265591 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
265543 TTTTCCTTAT
*
265553 TTTCTTTTGTTCTTC
1 TTTCTTTT-TTCTCC
265568 TTTCTTTTTT-TCC
1 TTTCTTTTTTCTCC
265581 TTTCTTTTTTC
1 TTTCTTTTTTC
265592 ATTTTACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 2 0.09
15 8 0.36
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTTCTCC
Found at i:265585 original size:17 final size:17
Alignment explanation
Indices: 265540--265587 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
265530 TCATTCTCTT
265540 TTTTTTTCCTTAT-TTTC
1 TTTTTTTCCTT-TCTTTC
*
265557 TTTTGTT-C-TTCTTTC
1 TTTTTTTCCTTTCTTTC
265572 TTTTTTTCCTTTCTTT
1 TTTTTTTCCTTTCTTT
265588 TTTCATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.04
15 11 0.42
16 2 0.08
17 12 0.46
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTTTCCTTTCTTTC
Found at i:265621 original size:30 final size:29
Alignment explanation
Indices: 265570--265632 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
265560 TGTTCTTCTT
265570 TCTTTTTTTCCTTTCTTTTTTCATTTTAC
1 TCTTTTTTTCCTTTCTTTTTTCATTTTAC
* *
265599 TCTTTTTCTTCACTTT-TTTTTTCCTTTTTC
1 TCTTTTT-TTC-CTTTCTTTTTTCATTTTAC
265629 TCTT
1 TCTT
265633 CACCATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 7 0.23
30 19 0.63
31 4 0.13
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (29 bp):
TCTTTTTTTCCTTTCTTTTTTCATTTTAC
Found at i:266046 original size:27 final size:28
Alignment explanation
Indices: 265990--266049 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
265980 TTTCTTTCTT
*
265990 CTTTTTTTTTGTTTTTCGATTCTCTTGA
1 CTTTTTTTTTGTTTTTCGATTCTCTAGA
266018 CTTTTTTTTTGGCTTTTTC-ATT-TC-AGA
1 CTTTTTTTTT-G-TTTTTCGATTCTCTAGA
266045 CTTTT
1 CTTTT
266050 ATTGTTTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.24
28 12 0.41
29 4 0.14
30 6 0.21
ACGTcount: A:0.08, C:0.15, G:0.10, T:0.67
Consensus pattern (28 bp):
CTTTTTTTTTGTTTTTCGATTCTCTAGA
Found at i:268329 original size:20 final size:20
Alignment explanation
Indices: 268304--268363 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
268294 TGGGATTTCT
268304 TTTGCATCATAAGACTTATC
1 TTTGCATCATAAGACTTATC
268324 TTTGCATCATAAGACTTATC
1 TTTGCATCATAAGACTTATC
268344 TTTGCATCATAAGACTTATC
1 TTTGCATCATAAGACTTATC
268364 CTTACTTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTGCATCATAAGACTTATC
Found at i:272120 original size:19 final size:19
Alignment explanation
Indices: 272048--272127 Score: 99
Period size: 19 Copynumber: 4.2 Consensus size: 19
272038 TTGACCTAAA
272048 GTTTAGGGTTTCACCTAGG
1 GTTTAGGGTTTCACCTAGG
*
272067 ATTTTAGGGTTTC-CCTAGG
1 -GTTTAGGGTTTCACCTAGG
* * *
272086 GTTTAAGATTTTACCTAGG
1 GTTTAGGGTTTCACCTAGG
*
272105 GTTTAGGGTTTCACCTGGG
1 GTTTAGGGTTTCACCTAGG
272124 GTTT
1 GTTT
272128 CGGACTTGTG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
18 8 0.16
19 31 0.62
20 11 0.22
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (19 bp):
GTTTAGGGTTTCACCTAGG
Found at i:272208 original size:13 final size:13
Alignment explanation
Indices: 272146--272282 Score: 123
Period size: 13 Copynumber: 10.4 Consensus size: 13
272136 TGGGTTCTAA
*
272146 TTAGGGTTTCAACC
1 TTAGGGTTTCAA-T
*
272160 TTAGGGATTTTAAT
1 TTAGGG-TTTCAAT
*
272174 TTAGGGTTTCGA-
1 TTAGGGTTTCAAT
*
272186 TTAAGGTTTCAAT
1 TTAGGGTTTCAAT
*
272199 TTAGGGTTTCAGT
1 TTAGGGTTTCAAT
* *
272212 TTAGGATATCAAT
1 TTAGGGTTTCAAT
*
272225 TTAGGGTTTTAAT
1 TTAGGGTTTCAAT
* * *
272238 TTAAGATTTTAAT
1 TTAGGGTTTCAAT
* *
272251 CTTAGGGTTTTAGT
1 -TTAGGGTTTCAAT
272265 TTAGGGTTTCAAT
1 TTAGGGTTTCAAT
272278 TTAGG
1 TTAGG
272283 AATTTACGAA
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
12 10 0.10
13 62 0.63
14 22 0.22
15 5 0.05
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.46
Consensus pattern (13 bp):
TTAGGGTTTCAAT
Found at i:272256 original size:53 final size:51
Alignment explanation
Indices: 272171--272282 Score: 143
Period size: 53 Copynumber: 2.2 Consensus size: 51
272161 TAGGGATTTT
* *
272171 AATTTAGGGTTTCGATTAAGGTTTCAATTTAGGGTTTCAGTTTAGGATATC
1 AATTTAGGGTTTCAATTAAGATTTCAATTTAGGGTTTCAGTTTAGGATATC
* * * * *
272222 AATTTAGGGTTTTAATTTAAGATTTTAATCTTAGGGTTTTAGTTTAGGGTTTC
1 AATTTAGGGTTTCAA-TTAAGATTTCAAT-TTAGGGTTTCAGTTTAGGATATC
272275 AATTTAGG
1 AATTTAGG
272283 AATTTACGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 13 0.25
52 11 0.21
53 28 0.54
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.46
Consensus pattern (51 bp):
AATTTAGGGTTTCAATTAAGATTTCAATTTAGGGTTTCAGTTTAGGATATC
Found at i:274299 original size:21 final size:20
Alignment explanation
Indices: 274275--274318 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
274265 ATTTTTTTGG
274275 TATTTTTATTT-TTAAATTTTT
1 TATTTTTATTTATT--ATTTTT
274296 TATTTTTATTTATTATTTTT
1 TATTTTTATTTATTATTTTT
274316 TAT
1 TAT
274319 AGCCAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 11 0.50
22 2 0.09
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TATTTTTATTTATTATTTTT
Found at i:274300 original size:7 final size:7
Alignment explanation
Indices: 274277--274318 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
274267 TTTTTTGGTA
274277 TTTTTAT
1 TTTTTAT
*
274284 TTTTAAAT
1 TTTT-TAT
274292 TTTTTA-
1 TTTTTAT
274298 TTTTTAT
1 TTTTTAT
*
274305 TTATTAT
1 TTTTTAT
274312 TTTTTAT
1 TTTTTAT
274319 AGCCAACAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:274306 original size:13 final size:14
Alignment explanation
Indices: 274277--274315 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
274267 TTTTTTGGTA
274277 TTTTTATTTTTAAAT
1 TTTTTATTTTT-AAT
274292 TTTTTATTTTT-AT
1 TTTTTATTTTTAAT
*
274305 TTATTATTTTT
1 TTTTTATTTTT
274316 TATAGCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
15 11 0.48
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTTTAAT
Found at i:276715 original size:15 final size:15
Alignment explanation
Indices: 276670--276716 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
276660 AGTAAGAAAA
*
276670 TGCAAAAAAGTAAAG
1 TGCAAAAATGTAAAG
276685 TGCATGAAAATGTAAAG
1 TGCA--AAAATGTAAAG
*
276702 TGCAAAAATTTAAAG
1 TGCAAAAATGTAAAG
276717 AACAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.50
17 14 0.50
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.21
Consensus pattern (15 bp):
TGCAAAAATGTAAAG
Found at i:277288 original size:21 final size:20
Alignment explanation
Indices: 277262--277306 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
277252 ACCATTTGCA
*
277262 CAAATTGCACAAAAAATTCTC
1 CAAATTGCA-AAAAAATTATC
* *
277283 CAAATTGTATAAAAATTATC
1 CAAATTGCAAAAAAATTATC
277303 CAAA
1 CAAA
277307 ATTCCTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (20 bp):
CAAATTGCAAAAAAATTATC
Found at i:283208 original size:13 final size:13
Alignment explanation
Indices: 283190--283215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
283180 CTCGGGCCCC
283190 AAAATATCTCTAA
1 AAAATATCTCTAA
283203 AAAATATCTCTAA
1 AAAATATCTCTAA
283216 TTGAGTGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATCTCTAA
Found at i:283704 original size:21 final size:21
Alignment explanation
Indices: 283661--283706 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
283651 ACCATTAGCA
*
283661 CAAATTGCATAAAAAATCCTC
1 CAAATTGCATAAAAAATCATC
* *
283682 CAAATTGTATAAAAAATTATC
1 CAAATTGCATAAAAAATCATC
283703 CAAA
1 CAAA
283707 ATTCCTCACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.26
Consensus pattern (21 bp):
CAAATTGCATAAAAAATCATC
Found at i:284095 original size:16 final size:16
Alignment explanation
Indices: 284058--284103 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
284048 ATCCATAAGA
*
284058 AAAAAAATAAAATA-T
1 AAAAAAATAAAAAAGT
284073 AAAAAAATAAAAAAGT
1 AAAAAAATAAAAAAGT
* *
284089 AAGAAAAGAAAAAAG
1 AAAAAAATAAAAAAG
284104 ATAATCAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (16 bp):
AAAAAAATAAAAAAGT
Found at i:286523 original size:18 final size:19
Alignment explanation
Indices: 286483--286529 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
286473 AATGGCTGGT
286483 AAAATCGATCAACGGTCTA
1 AAAATCGATCAACGGTCTA
286502 AAAATCGATCAACGGTCTA
1 AAAATCGATCAACGGTCTA
286521 AAAATCGAT
1 AAAATCGAT
286530 TTAGGATGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (19 bp):
AAAATCGATCAACGGTCTA
Found at i:289071 original size:21 final size:21
Alignment explanation
Indices: 289045--289084 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
289035 CAAGACTTGG
*
289045 ATATCATCATCCAGGAATTGA
1 ATATCATCATCAAGGAATTGA
289066 ATATCATCATCAAGGAATT
1 ATATCATCATCAAGGAATT
289085 ATCGATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (21 bp):
ATATCATCATCAAGGAATTGA
Found at i:289892 original size:22 final size:23
Alignment explanation
Indices: 289876--289921 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
289866 ATAGGCTTGG
289876 GTACCAATTAATCTAGGCTTAAA
1 GTACCAATTAATCTAGGCTTAAA
* *
289899 GTGCCAGTTAATCTAGGCTTAAA
1 GTACCAATTAATCTAGGCTTAAA
289922 TCATATTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (23 bp):
GTACCAATTAATCTAGGCTTAAA
Found at i:292096 original size:17 final size:17
Alignment explanation
Indices: 292072--292112 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 17
292062 TTTTCCCTTA
292072 TTTCTTTTTTTTTTTTG
1 TTTCTTTTTTTTTTTTG
292089 ---CTTTTTTTTTTTTG
1 TTTCTTTTTTTTTTTTG
292103 TTTCTTTTTT
1 TTTCTTTTTT
292113 CAAATAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.67
17 7 0.33
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (17 bp):
TTTCTTTTTTTTTTTTG
Found at i:293479 original size:16 final size:15
Alignment explanation
Indices: 293454--293488 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
293444 AACAAAAATG
293454 TTTTGTTTTTACATT
1 TTTTGTTTTTACATT
*
293469 TTTTGGTTTTTTCATT
1 TTTT-GTTTTTACATT
293485 TTTT
1 TTTT
293489 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.77
Consensus pattern (15 bp):
TTTTGTTTTTACATT
Found at i:295444 original size:7 final size:7
Alignment explanation
Indices: 295432--295457 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
295422 TTTATCATAT
295432 TTATTTA
1 TTATTTA
295439 TTATTTA
1 TTATTTA
295446 TTATTTA
1 TTATTTA
295453 TTATT
1 TTATT
295458 ATTTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:297407 original size:11 final size:11
Alignment explanation
Indices: 297391--297416 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
297381 TTCACTTTGA
297391 AATTTAGTAAT
1 AATTTAGTAAT
297402 AATTTAGTAAT
1 AATTTAGTAAT
297413 AATT
1 AATT
297417 CCCTTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAGTAAT
Found at i:298250 original size:26 final size:27
Alignment explanation
Indices: 298200--298255 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
298190 GGTGGTTTAA
*
298200 TTTAAGGTTTTAGGTTTAACCTAGGGT
1 TTTAAGGTTTTAGGTTTAACCTAGGAT
* * *
298227 TTTAGGGTTTTA-GTTTCACTTAGGAT
1 TTTAAGGTTTTAGGTTTAACCTAGGAT
298253 TTT
1 TTT
298256 CTAACGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (27 bp):
TTTAAGGTTTTAGGTTTAACCTAGGAT
Found at i:298764 original size:11 final size:12
Alignment explanation
Indices: 298748--298777 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
298738 TCATTCTGAA
298748 TTTTTTGCTTGT
1 TTTTTTGCTTGT
298760 TTTTTTGCTT-T
1 TTTTTTGCTTGT
298771 TTTTTTG
1 TTTTTTG
298778 TTCTATCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (12 bp):
TTTTTTGCTTGT
Found at i:299547 original size:32 final size:31
Alignment explanation
Indices: 299492--299563 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
299482 ATTTATTTAA
299492 TTTTTAAATAATTTTTACATTTTATCTAGTT
1 TTTTTAAATAATTTTTACATTTTATCTAGTT
* * * * *
299523 TTTTTTAATGATTTTTATATTTTTAT-TTGGT
1 TTTTTAAATAATTTTTACA-TTTTATCTAGTT
299554 TTTTTAAATA
1 TTTTTAAATA
299564 GCCAACAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (31 bp):
TTTTTAAATAATTTTTACATTTTATCTAGTT
Found at i:299941 original size:20 final size:19
Alignment explanation
Indices: 299893--299943 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
299883 TTTTTTGTGT
299893 TTTTTTCA--TTTGTTTTA
1 TTTTTTCATTTTTGTTTTA
* *
299910 TTTTTTGTATTTTTGTTGTTG
1 TTTTTT-CATTTTTGTT-TTA
299931 TTTTTTCATTTTT
1 TTTTTTCATTTTT
299944 TTAGAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 6 0.22
18 1 0.04
20 12 0.44
21 8 0.30
ACGTcount: A:0.08, C:0.04, G:0.10, T:0.78
Consensus pattern (19 bp):
TTTTTTCATTTTTGTTTTA
Found at i:300385 original size:41 final size:40
Alignment explanation
Indices: 300283--300787 Score: 300
Period size: 41 Copynumber: 12.5 Consensus size: 40
300273 TGCCCGAAGA
* * * *
300283 TCTTAGAAAATCATTTAAAAATTCAA-AGTTTTGCTCAAGGG
1 TCTTTGAAAATCATTTAAAAATTTAAGA-TTTTACCCAA-GG
* * * *
300324 T-TTTGAAAATCCTTAAAAAATTTAAGATTTTGCCCATAAG
1 TCTTTGAAAATCATTTAAAAATTTAAGATTTTACCCA-AGG
* * * *
300364 T-TTTGGAAAATCATTCAAAAATGTAAAATTTTACCTAGAGG
1 TCTTT-GAAAATCATTTAAAAATTTAAGATTTTACCCA-AGG
* * ** *
300405 TC-TTGGAGATCATTTAAAGTTTTAAGATTTTGCCCGAAGG
1 TCTTTGAAAATCATTTAAAAATTTAAGATTTTACCC-AAGG
* * *
300445 TCTTTTG-AAATCATTTAAAAATCTAAGATTTTGCCTAAAGG
1 TC-TTTGAAAATCATTTAAAAATTTAAGATTTTACC-CAAGG
* * *
300486 TCTTTGAAAATCATTTAAAAATCTAAAATTTTATCCAGAGG
1 TCTTTGAAAATCATTTAAAAATTTAAGATTTTACCCA-AGG
* * * *
300527 TC-TTGGAGATCATTCAAATATTTAAGATTTTACCC-AGAG
1 TCTTTGAAAATCATTTAAAAATTTAAGATTTTACCCAAG-G
* * * *
300566 TGTTTGGAAATCATTTAAAAAATTGAA-ATTTCACCCAGAGG
1 TCTTTGAAAATCATTT-AAAAATTTAAGATTTTACCCA-AGG
300607 TCTTTGAAAATC-TTTCAAAAATTTTAA-ATTTTACCCAAAGG
1 TCTTTGAAAATCATTT-AAAAA-TTTAAGATTTTACCC-AAGG
* * *
300648 TCTTTTAAAATCATTTAAAAATTTAAAGA-TTTGCCTGAAGG
1 TCTTTGAAAATCATTTAAAAATTT-AAGATTTTACC-CAAGG
* * * * **
300689 TC-TTGGAAATCGTTTAAAAATCTAAAATGTTT-CTTAGAGG
1 TCTTTGAAAATCATTTAAAAATTTAAGAT-TTTACCCA-AGG
* * * * ** *
300729 TC-TTGAAGATCATTCAAAGATTTAAGATTTTTCTTAGAGA
1 TCTTTGAAAATCATTTAAAAATTTAAGATTTTACCCA-AGG
*
300769 TCTTTGGAAATCATTTAAA
1 TCTTTGAAAATCATTTAAA
300788 GTGTTAAAGT
Statistics
Matches: 367, Mismatches: 71, Indels: 52
0.75 0.14 0.11
Matches are distributed among these distances:
38 2 0.01
39 9 0.02
40 172 0.47
41 174 0.47
42 10 0.03
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (40 bp):
TCTTTGAAAATCATTTAAAAATTTAAGATTTTACCCAAGG
Found at i:300456 original size:122 final size:119
Alignment explanation
Indices: 300325--300709 Score: 368
Period size: 122 Copynumber: 3.2 Consensus size: 119
300315 GCTCAAGGGT
* * *
300325 TTTGAAAATCCTTAAAAAATTTAAGATTTTGCCCATAAGT-TTTGGAAAATCATTCAAAAATGTA
1 TTTGGAAATCATTAAAAAATTTAAGATTTTGCCCA-AAGTCTTT-GAAAATCATTCAAAAATCTA
300389 AAATTTTACCTAGAGGTCTTGGAGATCATTTAAAGTTTTAAGATTTTGCCCGAAGGTC
64 AAATTTTACC-AGAGGTCTTGGAGATCATTTAAA-TTTTAAGATTTTGCCCGAAGGTC
* * * * *
300447 TTTTGAAATCATTTAAAAATCTAAGATTTTGCCTAAAGGTCTTTGAAAATCATTTAAAAATCTAA
1 TTTGGAAATCATTAAAAAATTTAAGATTTTGCCCAAA-GTCTTTGAAAATCATTCAAAAATCTAA
* * *
300512 AATTTTATCCAGAGGTCTTGGAGATCATTCAAATATTTAAGATTTTACCC--AGAGTG
65 AATTTTA-CCAGAGGTCTTGGAGATCATTTAAAT-TTTAAGATTTTGCCCGAAG-GTC
* ** * * * *
300568 TTTGGAAATCATTTAAAAAATTGAA-ATTTCACCCAGAGGTCTTTGAAAATCTTTCAAAAATTTT
1 TTTGGAAATCA-TTAAAAAATTTAAGATTTTGCCCA-AAGTCTTTGAAAATCATTCAAAAATCTA
* ** * * *
300632 AAATTTTACCCAAAGGTCTTTTAAAATCATTTAAAAATTTAAAGA-TTTGCCTGAAGGTC
64 AAATTTTA-CCAGAGGTC-TTGGAGATCATTT--AAATTTTAAGATTTTGCCCGAAGGTC
* *
300691 -TTGGAAATCGTTTAAAAAT
1 TTTGGAAATCATTAAAAAAT
300710 CTAAAATGTT
Statistics
Matches: 216, Mismatches: 35, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
120 2 0.01
121 68 0.31
122 127 0.59
123 13 0.06
124 6 0.03
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (119 bp):
TTTGGAAATCATTAAAAAATTTAAGATTTTGCCCAAAGTCTTTGAAAATCATTCAAAAATCTAAA
ATTTTACCAGAGGTCTTGGAGATCATTTAAATTTTAAGATTTTGCCCGAAGGTC
Found at i:300921 original size:80 final size:81
Alignment explanation
Indices: 300445--301166 Score: 295
Period size: 80 Copynumber: 8.9 Consensus size: 81
300435 TGCCCGAAGG
* * * * * *
300445 TCTTTTGAAATCATTTAAAA-ATCTAAGATTTTGCCTAAAGGTCTTTGAAAATCATTTAAAAATC
1 TCTTTGGAAATCA-TTAAAAGATTTAAGATTTTGCTTGAAGGTC-TTGGAAATCATTCAAAAATC
* *
300509 TAAAATTTTA-TCCAGAGG
64 TAAAATTTTACT-TAGAGA
* * * * ** *
300527 TC-TTGGAGATCATTCAAATATTTAAGATTTTAC-CCAGAGTGT-TTGGAAATCATTTAAAAAAT
1 TCTTTGGAAATCATTAAAAGATTTAAGATTTTGCTTGA-AG-GTCTTGGAAATCA-TTCAAAAAT
* * ** *
300589 -TGAAATTTCACCCAGAGG
63 CTAAAATTTTACTTAGAGA
* * * *** ** *
300607 TCTTTGAAAATCTTTCAAAA-ATTTTAA-ATTTTACCCAAAGGTCTTTTAAAATCATTTAAAAAT
1 TCTTTGGAAATCATT-AAAAGA-TTTAAGATTTTGCTTGAAGGTC-TTGGAAATCATTCAAAAAT
* ** * *
300670 TTAAAGATTTGCCTGA-AGG
63 CTAAA-ATTTTACTTAGAGA
* * * *
300689 TC-TTGGAAATCGTTTAAAA-ATCTAAAATGTTT-CTT-AGAGGTCTT-GAAGATCATTCAAAGA
1 TCTTTGGAAATC-ATTAAAAGATTTAAGAT-TTTGCTTGA-AGGTCTTGGAA-ATCATTCAAAAA
* * *
300749 TTTAAGATTTTTCTTAGAGA
62 TCTAAAATTTTACTTAGAGA
* * * * * *
300769 TCTTTGGAAATCATTTAAAG-TGTTAA-AGTTTTGCCTAAAAGTCTTGAAAATCGTTCAAAAATC
1 TCTTTGGAAATCATTAAAAGAT-TTAAGA-TTTTGCTTGAAGGTCTTGGAAATCATTCAAAAATC
* *
300832 TAAATTTTTACTTGGAGA
64 TAAAATTTTACTTAGAGA
* * * *
300850 TC-TTGGAGATCATTCAAAGATTTAAGATTTTGCTTGAAGGTGTTGGAAATCATTTAAAAATCTA
1 TCTTTGGAAATCATTAAAAGATTTAAGATTTTGCTTGAAGGTCTTGGAAATCATTCAAAAATCTA
** * *
300914 AGGTTTTACAT-GAAGG
66 AAATTTTACTTAG-AGA
* * * * * * *
300930 TCTTTAGAAATCATAAAAAAAAAAAAATTAAGGTTTTGCTT-AGAGGTCTTAGAAAACATTCAAA
1 TCTTTGGAAATCAT-----TAAAAGATTTAAGATTTTGCTTGA-AGGTCTTGGAAATCATTCAAA
* * *
300994 AGTCTAAAATTTTGCCTAGA-A
60 AATCTAAAATTTTACTTAGAGA
* * * * * ** *
301015 GTC-TTGGAGATCATTCAAAGATTTAAGATTTTGCTCGGAGGTCATGGTGATCATTTAAAAATC-
1 -TCTTTGGAAATCATTAAAAGATTTAAGATTTTGCTTGAAGGTCTTGGAAATCATTCAAAAATCT
* *
301078 AAAAGTTTCACTTAGAGG
65 AAAA-TTTTACTTAGAGA
* * * * * *
301096 TCTTTGG-AATCATAAAAATAATTTAAGGTTTTGCTTGGAGGTCTTGGAAGT-TTTCAAAAATCT
1 TCTTTGGAAATCATTAAAA-GATTTAAGATTTTGCTTGAAGGTCTTGGAAATCATTCAAAAATCT
301159 AAAATTTT
65 AAAATTTT
301167 CCTAGAGGTC
Statistics
Matches: 483, Mismatches: 113, Indels: 90
0.70 0.16 0.13
Matches are distributed among these distances:
79 14 0.03
80 194 0.40
81 170 0.35
82 39 0.08
83 6 0.01
85 10 0.02
86 49 0.10
87 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (81 bp):
TCTTTGGAAATCATTAAAAGATTTAAGATTTTGCTTGAAGGTCTTGGAAATCATTCAAAAATCTA
AAATTTTACTTAGAGA
Found at i:300941 original size:121 final size:122
Alignment explanation
Indices: 300655--300941 Score: 343
Period size: 121 Copynumber: 2.4 Consensus size: 122
300645 AGGTCTTTTA
* * *
300655 AAATCATTTAAAAATTTAAAGATTTGCCTGAAGGTC-TTGGAAATCGTTTAAAAATCTAAAATGT
1 AAATCATTTAAAAATTTAAAGTTTTGCCTGAAGGTCTTTAGAAATCGTTCAAAAATCTAAAATGT
* * *
300719 TTCTTAGAGGTCTTGAAGATCATTCAAAGATTTAAGATTTTTCTTAGAGATCTTTGG
66 TTCTTAGAGATCTTGAAGATCATTCAAAGATTTAAGATTTTGCTTAGAGATCGTTGG
* * * * *
300776 AAATCATTT-AAAGTGTTAAAGTTTTGCCTAAAAGTCTTGA-AAATCGTTCAAAAATCT-AAATT
1 AAATCATTTAAAAAT-TTAAAGTTTTGCCTGAAGGTCTTTAGAAATCGTTCAAAAATCTAAAATG
* * *
300838 TTTACTTGGAGATCTTGGAGATCATTCAAAGATTTAAGATTTTGCTT-GAAGGT-GTTGG
65 TTT-CTTAGAGATCTTGAAGATCATTCAAAGATTTAAGATTTTGCTTAG-AGATCGTTGG
* * * *
300896 AAATCATTTAAAAATCTAAGGTTTTACATGAAGGTCTTTAGAAATC
1 AAATCATTTAAAAATTTAAAGTTTTGCCTGAAGGTCTTTAGAAATC
300942 ATAAAAAAAA
Statistics
Matches: 138, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
120 43 0.31
121 94 0.68
122 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (122 bp):
AAATCATTTAAAAATTTAAAGTTTTGCCTGAAGGTCTTTAGAAATCGTTCAAAAATCTAAAATGT
TTCTTAGAGATCTTGAAGATCATTCAAAGATTTAAGATTTTGCTTAGAGATCGTTGG
Found at i:301047 original size:40 final size:40
Alignment explanation
Indices: 300330--301048 Score: 311
Period size: 40 Copynumber: 17.7 Consensus size: 40
300320 AGGGTTTTGA
* * * * *
300330 AAATCCTTAAAAAATTTAAGATTTTGCCCATAAGTTTTGG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAAGTCTTGG
* * * *
300370 AAAATCATTCAAAAATGTAAAATTTTACCTAGAGGTCTTGG
1 -AAATCATTCAAAAATTTAAGATTTTGCCTAGAAGTCTTGG
* * ** * *
300411 AGATCATTTAAAGTTTTAAGATTTTGCC-CGAAGGTCTTTTG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAA-GTC-TTGG
* * *
300452 AAATCATTTAAAAATCTAAGATTTTGCCTA-AAGGTCTTTGA
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAA-GTC-TTGG
* * * * *
300493 AAATCATTTAAAAATCTAAAATTTTATCC-AGAGGTCTTGG
1 AAATCATTCAAAAATTTAAGATTTT-GCCTAGAAGTCTTGG
* * * * *
300533 AGATCATTCAAATATTTAAGATTTTACCCAG-AGTGTTTGG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAAGT-CTTGG
* * ** * * *
300573 AAATCATTTAAAAAATTGAA-ATTTCACCCAGAGGTCTTTGA
1 AAATCA-TTCAAAAATTTAAGATTTTGCCTAGAAGTC-TTGG
* * * **
300614 AAATCTTTCAAAAATTTTAA-ATTTTACCCA-AAGGTCTTTTA
1 AAATCATTCAAAAA-TTTAAGATTTTGCCTAGAA-GTC-TTGG
*
300655 AAATCATTTAAAAATTTAAAGA-TTTGCCT-GAAGGTCTTGG
1 AAATCATTCAAAAATTT-AAGATTTTGCCTAGAA-GTCTTGG
* * * * * *
300695 AAATCGTTTAAAAATCTAAAATGTTT-CTTAGAGGTCTT-G
1 AAATCATTCAAAAATTTAAGAT-TTTGCCTAGAAGTCTTGG
* * *
300734 AAGATCATTCAAAGATTTAAGATTTTTCTTAG-AGATCTTTGG
1 AA-ATCATTCAAAAATTTAAGATTTTGCCTAGAAG-TC-TTGG
* * * *
300776 AAATCATT-TAAAGTGTTAA-AGTTTTGCCTAAAAGTCTTGA
1 AAATCATTCAAAAAT-TTAAGA-TTTTGCCTAGAAGTCTTGG
* * ** * *
300816 AAATCGTTCAAAAATCTAA-ATTTTTACTTGGAGATCTTGG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAAG-TCTTGG
* * * *
300856 AGATCATTCAAAGATTTAAGATTTTG-CTTGAAGGTGTTGG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAA-GTCTTGG
* * * * * *
300896 AAATCATTTAAAAATCTAAGGTTTTACAT-GAAGGTCTTTAG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAA-GTC-TTGG
** * * * * *
300937 AAATCATAAAAAAAAAAAAATTAAGGTTTTGCTTAGAGGTCTTAG
1 AAATCAT-----TCAAAAATTTAAGATTTTGCCTAGAAGTCTTGG
* * * *
300982 AAAACATTCAAAAGTCTAAAATTTTGCCTAGAAGTCTTGG
1 AAATCATTCAAAAATTTAAGATTTTGCCTAGAAGTCTTGG
* *
301022 AGATCATTCAAAGATTTAAGATTTTGC
1 AAATCATTCAAAAATTTAAGATTTTGC
301049 TCGGAGGTCA
Statistics
Matches: 514, Mismatches: 126, Indels: 77
0.72 0.18 0.11
Matches are distributed among these distances:
39 24 0.05
40 243 0.47
41 207 0.40
42 9 0.02
45 10 0.02
46 19 0.04
47 2 0.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (40 bp):
AAATCATTCAAAAATTTAAGATTTTGCCTAGAAGTCTTGG
Found at i:301070 original size:166 final size:159
Alignment explanation
Indices: 300791--301178 Score: 418
Period size: 166 Copynumber: 2.4 Consensus size: 159
300781 ATTTAAAGTG
* * * * * * * * *
300791 TTAAAGTTTTGCCTAAAAGTCTTGAAAATCGTTCAAAAATCTAAATTTTTACTTGGAGATCTTGG
1 TTAAGGTTTTGCTTAGAGGTCTTGAAAA-CATTCAAAAATCTAAAATTTTCCTAGAAG-TCTTGG
* ** * * *
300856 AGATCATTCAAAGATTTAAGATTTTGCTTGAAGGTGTTGGAAATCATTTAAAAATCTAAGGTTTT
64 AGATCATTCAAAGATTTAAGATTTTGCTCGAAGGTCATGGAAATCATTTAAAAATCAAAAGTTTC
300921 ACATGA-AGGTCTTTAGAAATCATAAAAAAAAAAAAA
129 AC-TGAGAGGTCTTT-GAAATCAT----AAAAAAAAA
*
300957 TTAAGGTTTTGCTTAGAGGTCTTAGAAAACATTCAAAAGTCTAAAATTTTGCCTAGAAGTCTTGG
1 TTAAGGTTTTGCTTAGAGGTCTT-GAAAACATTCAAAAATCTAAAATTTT-CCTAGAAGTCTTGG
* **
301022 AGATCATTCAAAGATTTAAGATTTTGCTCGGAGGTCATGGTGATCATTTAAAAATCAAAAGTTTC
64 AGATCATTCAAAGATTTAAGATTTTGCTCGAAGGTCATGGAAATCATTTAAAAATCAAAAGTTTC
* * * *
301087 ACTTAGAGGTCTTTGGAATCATAAAAATAAT
129 ACTGAGAGGTCTTTGAAATCATAAAAAAAAA
* * *** *
301118 TTAAGGTTTTGCTTGGAGGTCTTGGAAGTTTTCAAAAATCTAAAATTTTCCTAGAGGTCTT
1 TTAAGGTTTTGCTTAGAGGTCTTGAAAACATTCAAAAATCTAAAATTTTCCTAGAAGTCTT
301179 CGCAAATCAC
Statistics
Matches: 189, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
159 11 0.06
160 21 0.11
161 29 0.15
165 9 0.05
166 109 0.58
167 10 0.05
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (159 bp):
TTAAGGTTTTGCTTAGAGGTCTTGAAAACATTCAAAAATCTAAAATTTTCCTAGAAGTCTTGGAG
ATCATTCAAAGATTTAAGATTTTGCTCGAAGGTCATGGAAATCATTTAAAAATCAAAAGTTTCAC
TGAGAGGTCTTTGAAATCATAAAAAAAAA
Found at i:301961 original size:21 final size:21
Alignment explanation
Indices: 301904--301961 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
301894 AGCTTTCATG
*
301904 CAATCATGCAACATATACCTTT
1 CAAT-ATGCAACATGTACCTTT
* *
301926 TAATATGCAGCATGTACCTTT
1 CAATATGCAACATGTACCTTT
*
301947 CAATATGCAAAATGT
1 CAATATGCAACATGT
301962 GTCTGGACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (21 bp):
CAATATGCAACATGTACCTTT
Found at i:303142 original size:16 final size:16
Alignment explanation
Indices: 303121--303218 Score: 54
Period size: 16 Copynumber: 5.7 Consensus size: 16
303111 CACTCAATCA
303121 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTTCTT
*
303137 TTTTTTCCTTTTGTTTCTCCCT
1 TTTTTT--TCTT-TTTCT---T
303159 TTTTTTTCTTTTTCCTT
1 TTTTTTTCTTTTT-CTT
* * *
303176 TTTTTTTGTTCTTCCT
1 TTTTTTTCTTTTTCTT
** *
303192 CATTTTTCTTCTTTC-A
1 TTTTTTTCTT-TTTCTT
303208 TTTTTTTCTTT
1 TTTTTTTCTTT
303219 CCTCTTTCCT
Statistics
Matches: 62, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
15 1 0.02
16 23 0.37
17 15 0.24
18 3 0.05
19 8 0.13
20 5 0.08
22 7 0.11
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTTTTCTTTTTCTT
Found at i:303217 original size:13 final size:14
Alignment explanation
Indices: 303191--303219 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
303181 TTGTTCTTCC
303191 TCATTTTTCTTCTT
1 TCATTTTTCTTCTT
303205 TCATTTTT-TTCTT
1 TCATTTTTCTTCTT
303218 TC
1 TC
303220 CTCTTTCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (14 bp):
TCATTTTTCTTCTT
Found at i:305267 original size:12 final size:12
Alignment explanation
Indices: 305250--305279 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
305240 GGAATACAAT
305250 TATTATTATTAC
1 TATTATTATTAC
305262 TATTATTATTAC
1 TATTATTATTAC
*
305274 CATTAT
1 TATTAT
305280 CATCATTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:305284 original size:3 final size:3
Alignment explanation
Indices: 305278--305528 Score: 297
Period size: 3 Copynumber: 83.7 Consensus size: 3
305268 TATTACCATT
* * * * *
305278 ATC ATC ATT ATC ATC GTC ATC ATC ATC GTC ATC ATC ATC GTC ATC ATT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * * *
305326 ATT ATT ATT ATC ATT ATC ATC ATT ATT ATTA AT- ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A-TC ATC ATC ATC ATC ATC
* *
305371 ATC ATC ATC ATC ATC ATC ATC ATC ATT ATC ATC ATC ATC ATT ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
305419 ATC ATC ATC ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
305467 ATC ACC ATC ATC ATA ATC ATT ATT ATC ATT ATC ATC ATC ATT ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
305515 ATC ATC ATC ATC AT
1 ATC ATC ATC ATC AT
305529 TATTATTAAA
Statistics
Matches: 216, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.01
3 212 0.98
4 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.01, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:307406 original size:27 final size:27
Alignment explanation
Indices: 307364--307429 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
307354 TAAGGTTTAA
*
307364 TTTAGGGTTTCAGGTTTCAACTATA-GT
1 TTTAGGGTTTCAGGTTTCAACCA-AGGT
* *
307391 TTTAGGGTTTCGGGTTTCACCCAAGGT
1 TTTAGGGTTTCAGGTTTCAACCAAGGT
307418 TTTAGGGTTTCA
1 TTTAGGGTTTCA
307430 TATCGAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (27 bp):
TTTAGGGTTTCAGGTTTCAACCAAGGT
Found at i:307481 original size:24 final size:24
Alignment explanation
Indices: 307449--307508 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
307439 TCACCTAGAG
*
307449 TTTAGGGTTTCACTTAGG-TTTCAT
1 TTTAAGGTTTCACTTAGGCTTT-AT
*
307473 TTTAAGGTTTCACTTAGGCTTTTT
1 TTTAAGGTTTCACTTAGGCTTTAT
307497 TTTAAGGTTTCA
1 TTTAAGGTTTCA
307509 TTTTAGAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (24 bp):
TTTAAGGTTTCACTTAGGCTTTAT
Found at i:307482 original size:13 final size:13
Alignment explanation
Indices: 307464--307513 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
307454 GGTTTCACTT
307464 AGGTTTCATTTTA
1 AGGTTTCATTTTA
*
307477 AGGTTTCA-CTT-
1 AGGTTTCATTTTA
*
307488 AGGCTTT-TTTTTA
1 AGG-TTTCATTTTA
307501 AGGTTTCATTTTA
1 AGGTTTCATTTTA
307514 GAGTTTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
11 3 0.10
12 10 0.34
13 16 0.55
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.54
Consensus pattern (13 bp):
AGGTTTCATTTTA
Found at i:311508 original size:11 final size:11
Alignment explanation
Indices: 311488--311519 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
311478 ATTCTTGAAC
*
311488 CTTTTCTTTTT
1 CTTTTTTTTTT
311499 CTTTTTTTTTT
1 CTTTTTTTTTT
311510 CTTTTTTTTT
1 CTTTTTTTTT
311520 CTTATGGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:311514 original size:10 final size:10
Alignment explanation
Indices: 311488--311522 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
311478 ATTCTTGAAC
311488 CTTTTCTTTTT
1 CTTTT-TTTTT
311499 CTTTTTTTTTT
1 C-TTTTTTTTT
311510 CTTTTTTTTT
1 CTTTTTTTTT
311520 CTT
1 CTT
311523 ATGGATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 12 0.52
11 7 0.30
12 4 0.17
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:315130 original size:13 final size:13
Alignment explanation
Indices: 315112--315145 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
315102 ATTATGCCAC
315112 CACCATGGTCCCA
1 CACCATGGTCCCA
315125 CACCATGGTCCCA
1 CACCATGGTCCCA
315138 CACCATGG
1 CACCATGG
315146 CTTTTGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.15
Consensus pattern (13 bp):
CACCATGGTCCCA
Found at i:322364 original size:9 final size:8
Alignment explanation
Indices: 322336--322390 Score: 56
Period size: 9 Copynumber: 6.4 Consensus size: 8
322326 GCTGAGACAT
322336 TTTATTGTA
1 TTTATT-TA
*
322345 TTTGTTATA
1 TTTATT-TA
322354 TTTATTGTA
1 TTTATT-TA
*
322363 TTTGTTATA
1 TTTATT-TA
322372 TTTATTTA
1 TTTATTTA
322380 TTTATTTA
1 TTTATTTA
322388 TTT
1 TTT
322391 TTGAAATATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
8 13 0.33
9 26 0.67
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (8 bp):
TTTATTTA
Found at i:322377 original size:4 final size:4
Alignment explanation
Indices: 322336--322390 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
322326 GCTGAGACAT
* *
322336 TTTA TTGTA TTTG TTATA TTTA TTGTA TTTG TTATA TTTA TTTA TTTA
1 TTTA TT-TA TTTA TT-TA TTTA TT-TA TTTA TT-TA TTTA TTTA TTTA
322384 TTTA TTT
1 TTTA TTT
322391 TTGAAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
4 29 0.67
5 14 0.33
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:322388 original size:18 final size:18
Alignment explanation
Indices: 322336--322382 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
322326 GCTGAGACAT
322336 TTTATTGTATTTGTTATA
1 TTTATTGTATTTGTTATA
322354 TTTATTGTATTTGTTATA
1 TTTATTGTATTTGTTATA
322372 TTTATT-TATTT
1 TTTATTGTATTT
322383 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 5 0.17
18 24 0.83
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (18 bp):
TTTATTGTATTTGTTATA
Found at i:324457 original size:44 final size:44
Alignment explanation
Indices: 324298--324449 Score: 153
Period size: 44 Copynumber: 3.4 Consensus size: 44
324288 TAATCATTGG
* * *
324298 ACTTTGTGCATTTGTACAATTTCAATTGTTATATTGTTTGTTTA
1 ACTTTGTGCATTTGCACAATTTCAATTGTCATATTGTTTATTTA
** *
324342 ACTTTGCACATTTGCATC-ATTTCAATTGTCTTATTGTTTGTTTATTTA
1 ACTTTGTGCATTTGCA-CAATTTCAATTGTC--A-T-ATTGTTTATTTA
* ** *
324390 ACTTTGTTCATTTGCACTGTTTTAATTGTCATATTGTTTATTTA
1 ACTTTGTGCATTTGCACAATTTCAATTGTCATATTGTTTATTTA
*
324434 ACCTTGTGCATTTGCA
1 ACTTTGTGCATTTGCA
324450 TCATTTTATC
Statistics
Matches: 89, Mismatches: 13, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
44 49 0.55
45 2 0.02
46 2 0.02
47 2 0.02
48 34 0.38
ACGTcount: A:0.21, C:0.13, G:0.12, T:0.53
Consensus pattern (44 bp):
ACTTTGTGCATTTGCACAATTTCAATTGTCATATTGTTTATTTA
Found at i:326607 original size:26 final size:26
Alignment explanation
Indices: 326578--326633 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
326568 ATCATCAATT
*
326578 CTTAATTGTCATAAAAGCATTAGTAC
1 CTTAATTGTCATAAAAGCATCAGTAC
*
326604 CTTAATTGTCATAATAGCATCAGTAC
1 CTTAATTGTCATAAAAGCATCAGTAC
326630 CTTA
1 CTTA
326634 TCACATAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (26 bp):
CTTAATTGTCATAAAAGCATCAGTAC
Found at i:327118 original size:96 final size:96
Alignment explanation
Indices: 326942--327129 Score: 268
Period size: 96 Copynumber: 2.0 Consensus size: 96
326932 TTTCATTCTT
* * * * *
326942 TTCAATTGGAAGATTAAGAACCTTGATAATCTTTAAGGACAAAAGCTTCAGAACTTCACCCTACT
1 TTCAATTGGAAGATTAAAAACCTTAAGAATCTTTAAAGACAAAAGCTTCAGAACTTCACCCCACT
* *
327007 TGATCAAGATAAACCTTAAAAATTATTAATG
66 TGACCAAGACAAACCTTAAAAATTATTAATG
* * *
327038 TTCACTTGGAAGATTAAAAACCTTAAGAATCTTTAAAGACAAAAGCTTTAGAATTTCACCCCACT
1 TTCAATTGGAAGATTAAAAACCTTAAGAATCTTTAAAGACAAAAGCTTCAGAACTTCACCCCACT
* *
327103 TGACCATGACGAACCTTAAAAATTATT
66 TGACCAAGACAAACCTTAAAAATTATT
327130 GATCTTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 80 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (96 bp):
TTCAATTGGAAGATTAAAAACCTTAAGAATCTTTAAAGACAAAAGCTTCAGAACTTCACCCCACT
TGACCAAGACAAACCTTAAAAATTATTAATG
Found at i:328090 original size:21 final size:21
Alignment explanation
Indices: 328064--328116 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
328054 TATATGCATT
328064 TTATTTATCTTATTT-GTTTAG
1 TTATTTATCTTATTTAGTTT-G
*
328085 TTATTTCATCTTTTTTAGTTTG
1 TTATTT-ATCTTATTTAGTTTG
*
328107 TTCTTTATCT
1 TTATTTATCT
328117 GGTTAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 14 0.50
23 4 0.14
ACGTcount: A:0.15, C:0.09, G:0.08, T:0.68
Consensus pattern (21 bp):
TTATTTATCTTATTTAGTTTG
Found at i:328728 original size:21 final size:20
Alignment explanation
Indices: 328690--328729 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
328680 TTTGCAAAGA
* *
328690 TTTTTTGGATTTCTAAAATT
1 TTTTTTGGAATTCCAAAATT
328710 TTTTTTGGAAATTCCAAAAT
1 TTTTTTGG-AATTCCAAAAT
328730 CCAACAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (20 bp):
TTTTTTGGAATTCCAAAATT
Found at i:335528 original size:40 final size:40
Alignment explanation
Indices: 335473--335552 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
335463 TTTTTGTTAC
335473 TTAGTTGCTTCATATTAAACTTTGTATGATATTCATTAAG
1 TTAGTTGCTTCATATTAAACTTTGTATGATATTCATTAAG
* *
335513 TTAGTTGCTTCATATTGAACTTTGTATTATATTCATTAAG
1 TTAGTTGCTTCATATTAAACTTTGTATGATATTCATTAAG
335553 GCTAGGCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (40 bp):
TTAGTTGCTTCATATTAAACTTTGTATGATATTCATTAAG
Found at i:336665 original size:55 final size:56
Alignment explanation
Indices: 336570--336679 Score: 141
Period size: 55 Copynumber: 2.0 Consensus size: 56
336560 CACAATAAAA
* **
336570 CATGCAGGGTACATTGAGCATGTTAGCATTGAAGCCTTAACAAAATAAAATGATGG
1 CATGCAAGGTACATTGAGCATGTTAGCATAAAAGCCTTAACAAAATAAAATGATGG
** * * *
336626 CATGCAAGGT-CATTGAGCATGTTAGTGTAAAAGCTTTAACACACTAAAATGATG
1 CATGCAAGGTACATTGAGCATGTTAGCATAAAAGCCTTAACAAAATAAAATGATG
336680 ACTAAATTGC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
55 37 0.80
56 9 0.20
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (56 bp):
CATGCAAGGTACATTGAGCATGTTAGCATAAAAGCCTTAACAAAATAAAATGATGG
Found at i:343359 original size:15 final size:15
Alignment explanation
Indices: 343339--343382 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
343329 AACAAACTTT
* *
343339 TTTATAGAATAACTG
1 TTTATAGAACAACTA
343354 TTTATAGAACAACTA
1 TTTATAGAACAACTA
343369 TTTA-AGGAACAACT
1 TTTATA-GAACAACT
343383 TCTTTAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 25 0.96
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (15 bp):
TTTATAGAACAACTA
Found at i:348810 original size:1 final size:1
Alignment explanation
Indices: 348804--348829 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
348794 TAATAAAACT
348804 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
348830 GGAAAACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:350183 original size:30 final size:29
Alignment explanation
Indices: 350120--350183 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
350110 TTTTGAGTTA
* *
350120 TTAATATTTTATTGCAATCAATTAATCTT
1 TTAATATTTTATTGCAATCAATAAATCTC
350149 TTAATATTTTATTTTG-AATCAATCAAAT-TC
1 TTAATATTTTA--TTGCAATCAAT-AAATCTC
350179 TTAAT
1 TTAAT
350184 TAAACAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 11 0.37
30 13 0.43
31 6 0.20
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.52
Consensus pattern (29 bp):
TTAATATTTTATTGCAATCAATAAATCTC
Found at i:350730 original size:2 final size:2
Alignment explanation
Indices: 350723--350751 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
350713 GTAAAGCTAG
350723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
350752 ATGGATGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:354022 original size:9 final size:9
Alignment explanation
Indices: 354008--354082 Score: 64
Period size: 9 Copynumber: 8.3 Consensus size: 9
353998 TGCCTCCCTC
354008 AAAAGATGG
1 AAAAGATGG
354017 AAAAGATGG
1 AAAAGATGG
*
354026 AAAAGAAGG
1 AAAAGATGG
*
354035 CAAAGATGG
1 AAAAGATGG
* * *
354044 CAAGGAAGG
1 AAAAGATGG
*
354053 -CAAGAATGG
1 AAAAG-ATGG
354062 AAAAGA-GG
1 AAAAGATGG
354070 AAAAAGATGG
1 -AAAAGATGG
354080 AAA
1 AAA
354083 GAAAGACAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
8 4 0.08
9 44 0.83
10 5 0.09
ACGTcount: A:0.56, C:0.04, G:0.33, T:0.07
Consensus pattern (9 bp):
AAAAGATGG
Found at i:354031 original size:18 final size:18
Alignment explanation
Indices: 354008--354082 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
353998 TGCCTCCCTC
*
354008 AAAAGATGGAAAAGATGG
1 AAAAGAAGGAAAAGATGG
*
354026 AAAAGAAGGCAAAGATGG
1 AAAAGAAGGAAAAGATGG
* * *
354044 CAAGGAAGG-CAAGAATGG
1 AAAAGAAGGAAAAG-ATGG
354062 AAAAG-AGGAAAAAGATGG
1 AAAAGAAGG-AAAAGATGG
354080 AAA
1 AAA
354083 GAAAGACAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.13
18 37 0.80
19 3 0.07
ACGTcount: A:0.56, C:0.04, G:0.33, T:0.07
Consensus pattern (18 bp):
AAAAGAAGGAAAAGATGG
Found at i:354076 original size:36 final size:35
Alignment explanation
Indices: 354022--354103 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
354012 GATGGAAAAG
* * * *
354022 ATGGAAAAGAAGGCAAAGATGGCAAGGAAGGCAAGA
1 ATGGAAAAG-AGGAAAAGATGGAAAGAAAGACAAGA
354058 ATGGAAAAGAGGAAAAAGATGGAAAGAAAGACAAGA
1 ATGGAAAAGAGG-AAAAGATGGAAAGAAAGACAAGA
*
354094 ACGGAAAAGA
1 ATGGAAAAGA
354104 TGCAAAGGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 3 0.08
36 37 0.93
ACGTcount: A:0.56, C:0.06, G:0.33, T:0.05
Consensus pattern (35 bp):
ATGGAAAAGAGGAAAAGATGGAAAGAAAGACAAGA
Found at i:357169 original size:21 final size:22
Alignment explanation
Indices: 357130--357170 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
357120 AATTTAAAAT
*
357130 TTTAATAAAAATTGTATATGAA
1 TTTAATAAAAATAGTATATGAA
357152 TTTAATAAAAATAG-ATATG
1 TTTAATAAAAATAGTATATG
357171 TATATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
TTTAATAAAAATAGTATATGAA
Found at i:359916 original size:1 final size:1
Alignment explanation
Indices: 359910--359935 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
359900 AAATTGTTGG
359910 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
359936 CAGGGCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:362208 original size:2 final size:2
Alignment explanation
Indices: 362201--362230 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
362191 AACATGCACG
*
362201 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
362231 GAATTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:363529 original size:19 final size:19
Alignment explanation
Indices: 363462--363521 Score: 111
Period size: 19 Copynumber: 3.2 Consensus size: 19
363452 TGAGAAATTC
*
363462 TTGAAAATATTCCAATATT
1 TTGAAAATATTCAAATATT
363481 TTGAAAATATTCAAATATT
1 TTGAAAATATTCAAATATT
363500 TTGAAAATATTCAAATATT
1 TTGAAAATATTCAAATATT
363519 TTG
1 TTG
363522 GCAATATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (19 bp):
TTGAAAATATTCAAATATT
Found at i:364865 original size:21 final size:21
Alignment explanation
Indices: 364840--364880 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
364830 TGTTTGTATA
* *
364840 GAAAATTGCTACTAATTTAGT
1 GAAAAATGCCACTAATTTAGT
364861 GAAAAATGCCACTAATTTAG
1 GAAAAATGCCACTAATTTAG
364881 CGGCATTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (21 bp):
GAAAAATGCCACTAATTTAGT
Found at i:364922 original size:34 final size:35
Alignment explanation
Indices: 364884--364977 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 35
364874 AATTTAGCGG
*
364884 CATTTGTATAG-GA-AAACACCCTTAAATTTAATGA
1 CATTT-TATAGCGACAAACACCCCTAAATTTAATGA
* *
364918 CATTTTAT-GCTACAAACACCCCTAAATTTAATGG
1 CATTTTATAGCGACAAACACCCCTAAATTTAATGA
* *
364952 CATTTTATA-CTACAAACACCACTAAA
1 CATTTTATAGCGACAAACACCCCTAAA
364978 ATTTGAATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
32 1 0.02
33 4 0.08
34 48 0.91
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (35 bp):
CATTTTATAGCGACAAACACCCCTAAATTTAATGA
Found at i:366484 original size:161 final size:161
Alignment explanation
Indices: 366263--367034 Score: 724
Period size: 161 Copynumber: 4.8 Consensus size: 161
366253 TCAATCATGA
* * * *
366263 AAACTAAGTTCAATCATTCGAA-AA-ATTAATATCATGTATTGAAGCCATCTAAACTGTTAAAAT
1 AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAAT
** ** ** *
366326 AGATTAATAACAACAAATTTGTATTTTTGCCTTTTAATGGCA-AAAATAGAACTAAATAGACGTA
66 AGAACAATAACAACAAATTTGTATTTTTGCCTTTTAACAGCATAAAATAGTCCTAAACAGACGTA
366390 AATGATAACTTTTTCACACATATCAACTGTAG
131 AATGATAACTTTTTCACACATATCAACTGT-G
*
366422 AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAATTGTTAAAAT
1 AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAAT
* * * **
366487 AGAACAATAATATC-AATTT-TACATTTTGCCTTTTAATGGCATAAAAT-GTCCTAAACAGACGT
66 AGAACAATAACAACAAATTTGTA-TTTTTGCCTTTTAACAGCATAAAATAGTCCTAAACAGACGT
* * * *
366549 AAA-CATTAGC-TTTTCACATATATCAACTATG
130 AAATGA-TAACTTTTTCACACATATCAACTGTG
* * * * ** *
366580 AAAACCAATTTCAATTATTCTG-ACCAGTTTAATATCATGTATTAAAGCTAGGCAAACTATTAAA
1 -AAACCAAGTTCAATCATTC-GAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAA
* * * *
366644 ATAGAACAATAACAACAAATTTGCATGTTTGCCTTTTAACAACATAAAA-AGTCTTAAACAGACG
64 ATAGAACAATAACAACAAATTTGTATTTTTGCCTTTTAACAGCATAAAATAGTCCTAAACAGACG
* *
366708 TAAACGATAACTTTTTCACACATATCAATTGTG
129 TAAATGATAACTTTTTCACACATATCAACTGTG
* * * * *
366741 TAAATCAAGTTCAATTATTCGGACAAGTTTAATATCATGTATTGGAGCAATCCAAACTGTTAAAA
1 -AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAA
***** * * ** * *
366806 TAGAACAATTTGTCCAAATTTATATTTTTACCTAATAACAGCACAAAATA-TCCTAAATAGACGT
65 TAGAACAATAACAACAAATTTGTATTTTTGCCTTTTAACAGCATAAAATAGTCCTAAACAGACGT
* * * *
366870 AAATAATAACTTTTTTATACATATTAA-TCGTGG
130 AAATGATAACTTTTTCACACATATCAACT-GT-G
* * * * * * * * *
366903 AAACTAAGGTCAATAATTTGGATAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAAT
1 AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAAT
* * * * * * * ** *
366968 AGAACAATAACTATAAATTTGCATTATTACCTTGTAACAGCACAAAA-AGTTGTAAACAGACATA
66 AGAACAATAACAACAAATTTGTATTTTTGCCTTTTAACAGCATAAAATAGTCCTAAACAGACGTA
367032 AAT
131 AAT
367035 TGCAAATTAC
Statistics
Matches: 502, Mismatches: 94, Indels: 32
0.80 0.15 0.05
Matches are distributed among these distances:
158 1 0.00
159 109 0.22
160 91 0.18
161 299 0.60
162 2 0.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (161 bp):
AAACCAAGTTCAATCATTCGAACAAGTTTAATATCATGTATTGAAGCTATCCAAACTGTTAAAAT
AGAACAATAACAACAAATTTGTATTTTTGCCTTTTAACAGCATAAAATAGTCCTAAACAGACGTA
AATGATAACTTTTTCACACATATCAACTGTG
Found at i:368216 original size:13 final size:13
Alignment explanation
Indices: 368181--368217 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
368171 ATATAAGTGA
*
368181 ATATATAAAAAAC
1 ATATATAAAGAAC
*
368194 ATATGTAAAGAAC
1 ATATATAAAGAAC
368207 ATATATAAAGA
1 ATATATAAAGA
368218 CATTGAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:371230 original size:14 final size:16
Alignment explanation
Indices: 371206--371241 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
371196 AGCTGTTTTC
371206 TATTT-TTTGG-TATT
1 TATTTATTTGGTTATT
371220 T-TTTATTTGGTTATT
1 TATTTATTTGGTTATT
371235 TATTTAT
1 TATTTAT
371242 ATTCCATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.16
14 6 0.32
15 5 0.26
16 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (16 bp):
TATTTATTTGGTTATT
Found at i:371407 original size:231 final size:230
Alignment explanation
Indices: 371004--371453 Score: 855
Period size: 231 Copynumber: 2.0 Consensus size: 230
370994 AGATTATTGC
*
371004 TATTTATATTCCATCAAAATAACATTGTTTTAGCATTAAGAAACCACCTAGGATCTGCGTGTTTT
1 TATTTATATTCCATCAAAATAACATTGTTTTAGCATTAAGAAACCACCTAGGATCTGCGTGCTTT
* *
371069 TATTTGAGTGACTTGACCCACGCGCAACTAGCTTCTACCGACTAGTTTTCCAGTCCATTCCTTCA
66 TATCTGAGTGACTTGACCCACGCGCAACTAGCTTCTACCGACTAGTTTTCCAGTCCACTCCTTCA
*
371134 ACCGAGCCAAGCGGAGCCCCAAGTCGCTTCTTTGGAGCTGAGCCACGTCGAGTCTTTAGCCAAGC
131 ACCGAGCCAAGCCGAGCCCCAAGTCGCTTCTTTGGAGCTGAGCCACGTCGAGTCTTTAGCCAAGC
371199 TGTTTTCTATTTTTTGGTATTTTTTATTTGGTTATT
196 TGTTTTCTATTTTTT-GTATTTTTTATTTGGTTATT
371235 TATTTATATTCCATCAAAATAACATTGTTTTAGCATTAAGAAACCACCTAGGATCTGCGTGCTTT
1 TATTTATATTCCATCAAAATAACATTGTTTTAGCATTAAGAAACCACCTAGGATCTGCGTGCTTT
371300 TATCTGAGTGACTTGACCCACGCGCAACTAGCTTCTACCGACTAGTTTTCCAGTCCACTCCTTCA
66 TATCTGAGTGACTTGACCCACGCGCAACTAGCTTCTACCGACTAGTTTTCCAGTCCACTCCTTCA
371365 ACCGAGCCAAGCCGAGCCCCAAGTCGCTTCTTTGGAGCTGAGCCACGTCGAGTCTTTAGCCAAGC
131 ACCGAGCCAAGCCGAGCCCCAAGTCGCTTCTTTGGAGCTGAGCCACGTCGAGTCTTTAGCCAAGC
371430 TGTTTTCTATTTTTTGTATTTTTT
196 TGTTTTCTATTTTTTGTATTTTTT
371454 TGGTTTTTTT
Statistics
Matches: 215, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
230 9 0.04
231 206 0.96
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.35
Consensus pattern (230 bp):
TATTTATATTCCATCAAAATAACATTGTTTTAGCATTAAGAAACCACCTAGGATCTGCGTGCTTT
TATCTGAGTGACTTGACCCACGCGCAACTAGCTTCTACCGACTAGTTTTCCAGTCCACTCCTTCA
ACCGAGCCAAGCCGAGCCCCAAGTCGCTTCTTTGGAGCTGAGCCACGTCGAGTCTTTAGCCAAGC
TGTTTTCTATTTTTTGTATTTTTTATTTGGTTATT
Found at i:371822 original size:26 final size:26
Alignment explanation
Indices: 371793--371855 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
371783 AAGAATGAGA
*
371793 TTCTTAGAAATTTCAAATAATAAATT
1 TTCTAAGAAATTTCAAATAATAAATT
**
371819 TTCTAAGAAATTTCAAATGGTAAATT
1 TTCTAAGAAATTTCAAATAATAAATT
371845 TTCTAAGAAAT
1 TTCTAAGAAAT
371856 CTCTAGGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (26 bp):
TTCTAAGAAATTTCAAATAATAAATT
Found at i:373274 original size:29 final size:29
Alignment explanation
Indices: 373232--373299 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
373222 GTTCAAGAAT
373232 AACTCACCAAGCAAGAACCCTACACAACC
1 AACTCACCAAGCAAGAACCCTACACAACC
373261 AACTCACCAAGCAAGAACCCTACACAACC
1 AACTCACCAAGCAAGAACCCTACACAACC
373290 AACTCACCAA
1 AACTCACCAA
373300 TACAATACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.46, C:0.41, G:0.06, T:0.07
Consensus pattern (29 bp):
AACTCACCAAGCAAGAACCCTACACAACC
Found at i:375794 original size:20 final size:20
Alignment explanation
Indices: 375756--375797 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
375746 TTTTCATTCA
375756 TCAAATCATCAAATTTCTTTT
1 TCAAATCA-CAAATTTCTTTT
375777 TCAAATCA-AAATTTTCTTTT
1 TCAAATCACAAA-TTTCTTTT
375797 T
1 T
375798 ATAAAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 9 0.45
21 8 0.40
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (20 bp):
TCAAATCACAAATTTCTTTT
Found at i:377326 original size:21 final size:21
Alignment explanation
Indices: 377302--377345 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
377292 ATTGGTTTAG
*
377302 CTAGGGGATCGATCCTGTAAC
1 CTAGGGGATCGATCCTATAAC
* *
377323 CTAGGGGATTGATCTTATAAC
1 CTAGGGGATCGATCCTATAAC
377344 CT
1 CT
377346 TGCTTTGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
CTAGGGGATCGATCCTATAAC
Found at i:379577 original size:63 final size:63
Alignment explanation
Indices: 379393--379578 Score: 189
Period size: 63 Copynumber: 3.0 Consensus size: 63
379383 TTTTTAGTTA
* * * * *
379393 GAAAACACCTTCAATAATCCCTTATAAAAATTTATTGAGTGGATTATTGAAGGCA-TTTTCAGC
1 GAAAATACCTTCAATAATCCCTTCT-AAAATTTTTTGAATGGATTATTGAAGGCATTTTTTAGC
* * ** * ** *
379456 TAAAAATGCCTTCAATAATCCCTTCT-AAATTTTTTCTATGAATTATTGAAGGTTTTTTTTTG-
1 -GAAAATACCTTCAATAATCCCTTCTAAAATTTTTTGAATGGATTATTGAAGGCATTTTTTAGC
* *
379518 GAAAATACCTTCAATATTCTCTCTCTAAAATTTTTTGAATGGATTATTGAAGGCATTTTTT
1 GAAAATACCTTCAATAATCCCT-TCTAAAATTTTTTGAATGGATTATTGAAGGCATTTTTT
379579 GGCAAAAAAA
Statistics
Matches: 97, Mismatches: 22, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
61 18 0.19
62 24 0.25
63 34 0.35
64 21 0.22
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (63 bp):
GAAAATACCTTCAATAATCCCTTCTAAAATTTTTTGAATGGATTATTGAAGGCATTTTTTAGC
Found at i:380805 original size:9 final size:9
Alignment explanation
Indices: 380785--380825 Score: 64
Period size: 9 Copynumber: 4.3 Consensus size: 9
380775 CGTAACTTTC
380785 TTTCTTTTTT
1 TTTC-TTTTT
380795 TTTCCTTTTT
1 TTT-CTTTTT
380805 TTTCTTTTT
1 TTTCTTTTT
380814 TTTCTTTTT
1 TTTCTTTTT
380823 TTT
1 TTT
380826 TCTTATTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 18 0.60
10 11 0.37
11 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:380817 original size:19 final size:19
Alignment explanation
Indices: 380785--380829 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
380775 CGTAACTTTC
380785 TTTCTTTTTTTTTCCTTTTT
1 TTTC-TTTTTTTTCCTTTTT
*
380805 TTTCTTTTTTTTCTTTTTT
1 TTTCTTTTTTTTCCTTTTT
380824 TTTCTT
1 TTTCTT
380830 ATTTGGTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTCTTTTTTTTCCTTTTT
Found at i:380828 original size:10 final size:10
Alignment explanation
Indices: 380785--380829 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
380775 CGTAACTTTC
380785 TTTCTTTTTT
1 TTTCTTTTTT
*
380795 TTTCCTTTTT
1 TTTCTTTTTT
380805 TTTC-TTTTT
1 TTTCTTTTTT
380814 TTTCTTTTTT
1 TTTCTTTTTT
380824 TTTCTT
1 TTTCTT
380830 ATTTGGTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
9 9 0.27
10 24 0.73
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:381989 original size:12 final size:12
Alignment explanation
Indices: 381945--381991 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
381935 GTAATATAAA
*
381945 TTTAATTAATTA
1 TTTAATTAATTT
*
381957 ATTAATTAATTT
1 TTTAATTAATTT
*
381969 TTTTA-TAATTT
1 TTTAATTAATTT
381980 TTTAATTAATTT
1 TTTAATTAATTT
381992 GATTTATTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAATTAATTT
Found at i:382303 original size:26 final size:26
Alignment explanation
Indices: 382274--382323 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
382264 AAGTTTTCTC
* *
382274 TTTTTTTATTTTTTTTACTT-AATTGA
1 TTTTTTGAATTTTTTT-CTTGAATTGA
382300 TTTTTTGAATTTTTTTCTTGAATT
1 TTTTTTGAATTTTTTTCTTGAATT
382324 TAGGTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.72
Consensus pattern (26 bp):
TTTTTTGAATTTTTTTCTTGAATTGA
Found at i:382698 original size:22 final size:22
Alignment explanation
Indices: 382673--382718 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
382663 GATTTTATAG
* *
382673 ATTATGTCCAAAGGTCTTAGAA
1 ATTATATCCAAAGGTCTTACAA
* *
382695 ATTATATTCGAAGGTCTTACAA
1 ATTATATCCAAAGGTCTTACAA
382717 AT
1 AT
382719 CTTAAAATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
ATTATATCCAAAGGTCTTACAA
Found at i:382818 original size:22 final size:23
Alignment explanation
Indices: 382757--382811 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
382747 AGAGGCATTG
* * *
382757 CCCGGAGGTCTTATAGATTATGT
1 CCCGAAGGTCTTAAAGATTATGA
382780 CCC-AAGGTCTTAAAGATTAT-A
1 CCCGAAGGTCTTAAAGATTATGA
382801 CCCGAAGGTCT
1 CCCGAAGGTCT
382812 GAGAGATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (23 bp):
CCCGAAGGTCTTAAAGATTATGA
Found at i:382948 original size:22 final size:22
Alignment explanation
Indices: 382908--382988 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
382898 TATTGTGCCT
* *
382908 GAAGGTCTTACAAAATATGCTC
1 GAAGGTCTTAGAAATTATGCTC
*
382930 GAAGGTCTTAGATATTATGAC-C
1 GAAGGTCTTAGAAATTATG-CTC
* *
382952 -AGAGGTCTTAGAGATTATGTTC
1 GA-AGGTCTTAGAAATTATGCTC
* *
382974 GGAGGTCTTACAAAT
1 GAAGGTCTTAGAAAT
382989 ATCAAAATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
21 1 0.02
22 45 0.96
23 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (22 bp):
GAAGGTCTTAGAAATTATGCTC
Found at i:395099 original size:49 final size:46
Alignment explanation
Indices: 395022--395119 Score: 126
Period size: 45 Copynumber: 2.1 Consensus size: 46
395012 ACAATTTTAT
* * *
395022 AAATATTCAATTAAAATAAAAAAATTATGTAAAA-TTTATCACTTA
1 AAATATTCAATTAAAAAAAAAAAATTATGTAAAACTTCACCACTTA
395067 AAATATTCAATTACAATAAAAAAAAAATTTATGTAAAACTTCACCACTTA
1 AAATATTCAATT--AA-AAAAAAAAAA-TTATGTAAAACTTCACCACTTA
395117 AAA
1 AAA
395120 ACCTAAGCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
45 12 0.27
47 2 0.04
48 9 0.20
49 10 0.22
50 12 0.27
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (46 bp):
AAATATTCAATTAAAAAAAAAAAATTATGTAAAACTTCACCACTTA
Found at i:400242 original size:31 final size:31
Alignment explanation
Indices: 400194--400274 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
400184 TGATTGATTA
400194 AATTATG-ATTATTTGATTATTATATTTTATTG
1 AATTATGTATTA--TGATTATTATATTTTATTG
* * *
400226 AATTGTGTATTATGATTATTGTATTTTATTT
1 AATTATGTATTATGATTATTATATTTTATTG
*
400257 AATTATGTA-TATTATTAT
1 AATTATGTATTATGATTAT
400275 GTATTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 8 0.19
31 25 0.58
32 6 0.14
33 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (31 bp):
AATTATGTATTATGATTATTATATTTTATTG
Found at i:403270 original size:15 final size:16
Alignment explanation
Indices: 403250--403289 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
403240 GAACTCTTTG
*
403250 AAAAGAAAATA-ATAA
1 AAAAGAAAAGACATAA
403265 AAAAGAAAAGACATAA
1 AAAAGAAAAGACATAA
*
403281 AAAATAAAA
1 AAAAGAAAA
403290 AGATGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (16 bp):
AAAAGAAAAGACATAA
Found at i:403638 original size:20 final size:21
Alignment explanation
Indices: 403601--403642 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
403591 ATGGGAATAT
403601 AAATAATGAAAAAAGTGAAAA
1 AAATAATGAAAAAAGTGAAAA
* *
403622 AAAT-ATGAGAAAGGTGAAAA
1 AAATAATGAAAAAAGTGAAAA
403642 A
1 A
403643 TGAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (21 bp):
AAATAATGAAAAAAGTGAAAA
Found at i:405580 original size:14 final size:14
Alignment explanation
Indices: 405561--405613 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
405551 AACAATTAGA
405561 ATTGCATTCATAAC
1 ATTGCATTCATAAC
*
405575 ATTGCATTCAT-GC
1 ATTGCATTCATAAC
* *
405588 ACTGTATTCATAAAC
1 ATTGCATTCAT-AAC
*
405603 ATTGCACTCAT
1 ATTGCATTCAT
405614 GTAATTTGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 10 0.33
14 11 0.37
15 9 0.30
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (14 bp):
ATTGCATTCATAAC
Found at i:406386 original size:84 final size:82
Alignment explanation
Indices: 406244--406418 Score: 192
Period size: 84 Copynumber: 2.1 Consensus size: 82
406234 GGCATAATTT
* * *
406244 TAAGTCTTTCAAGTTGAATCTATTTAAATGTCGAGATTTGTAAAACCTTCGATTATAATCTCTAA
1 TAAGTC-TTCAAGTTGAATCTATTTAAATGTCAAGATTTATAAAACCTTCGATCATAATCTC-AA
* * *
406309 GTCTTCTAGGTAAGATTCA
64 ATCCTCTAAGTAAGATTCA
* * *
406328 TAAGTCTTCGAAGTTGAATCTGTTTAAGTGTCAAGATTTATAAGA-CTTCCG-TGCATAATCTCA
1 TAAGTCTTC-AAGTTGAATCTATTTAAATGTCAAGATTTATAAAACCTT-CGAT-CATAATCTCA
**
406391 AATCCTCTAAGTAAGATTTG
63 AATCCTCTAAGTAAGATTCA
406411 TAAGTCTT
1 TAAGTCTT
406419 TTGAGCTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
83 31 0.40
84 46 0.60
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (82 bp):
TAAGTCTTCAAGTTGAATCTATTTAAATGTCAAGATTTATAAAACCTTCGATCATAATCTCAAAT
CCTCTAAGTAAGATTCA
Found at i:408356 original size:31 final size:30
Alignment explanation
Indices: 408310--408397 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
408300 TGATTGATTA
408310 AATTATGATTATTTGATTATTGTATTTTATTG
1 AATTATG-TT-TTTGATTATTGTATTTTATTG
* * *
408342 AATTGTGTATTTTGATTATTGTATGTTATTT
1 AATTATGT-TTTTGATTATTGTATTTTATTG
408373 AATTATGTTTATT-ATTA-TGTATTTT
1 AATTATGTTT-TTGATTATTGTATTTT
408398 TTTCATAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
29 7 0.14
30 6 0.12
31 29 0.59
32 7 0.14
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.61
Consensus pattern (30 bp):
AATTATGTTTTTGATTATTGTATTTTATTG
Found at i:410457 original size:19 final size:18
Alignment explanation
Indices: 410420--410458 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
410410 TATGGTGAGA
* *
410420 TTTCTTCAAATTGTTTCT
1 TTTCTACAAATTCTTTCT
410438 TTTCTACAACATTCTTTCT
1 TTTCTACAA-ATTCTTTCT
410457 TT
1 TT
410459 GCTCTAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTCTACAAATTCTTTCT
Found at i:414626 original size:37 final size:37
Alignment explanation
Indices: 414581--414686 Score: 92
Period size: 38 Copynumber: 2.9 Consensus size: 37
414571 TTTTAAAAAG
*
414581 CTCCCCAAATAGAGGCTTTTGAACTTTAAAAATGGCT
1 CTCCCCAAATAGAGGCTTTTGAACTTTAAAAATAGCT
* * ** *
414618 TTCCCCAAACA-A-AATATTTGAAACTTTTGAAAATAGCT
1 CTCCCCAAATAGAGGCT-TTTG-AAC-TTTAAAAATAGCT
* *
414656 CCCCCCAAATAGAGGC-TTTGAAATTTAAAAA
1 CTCCCCAAATAGAGGCTTTTGAACTTTAAAAA
414687 AAAATTACTC
Statistics
Matches: 51, Mismatches: 13, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
35 1 0.02
36 12 0.24
37 14 0.27
38 23 0.45
39 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (37 bp):
CTCCCCAAATAGAGGCTTTTGAACTTTAAAAATAGCT
Found at i:414960 original size:105 final size:103
Alignment explanation
Indices: 414763--414962 Score: 269
Period size: 105 Copynumber: 1.9 Consensus size: 103
414753 TACAAATCTC
* *
414763 AAAATCTCTAAATGTTATCCTAATCAAAGGCAATGAAACTTTAAAAATTTAAAATATTTTGCTAG
1 AAAATCTCTAAATGTCATCCTAATCAAAGGCAATGAAACTTTAAAAATTTAAAAAATTTTGCTAG
414828 AGGTCTTGAAAATTGTGTCCAGAGGTCTTATAAGTTTT
66 AGGTCTTGAAAATTGTGTCCAGAGGTCTTATAAGTTTT
* * * *
414866 AAAATCTTTAAATGCTCATCC-AATCAGAGG-ATTGAAACTTTAACAATTTGAAAAAAGTTTTGC
1 AAAATCTCTAAATG-TCATCCTAATCAAAGGCAATGAAACTTTAAAAATTT-AAAAAA-TTTTGC
* **
414929 TCGAAGGTCTTGAAAATTGTGTTTAGAGGTCTTA
63 TAG-AGGTCTTGAAAATTGTGTCCAGAGGTCTTA
414963 GAGATTATAC
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
102 17 0.20
103 26 0.31
104 13 0.15
105 28 0.33
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (103 bp):
AAAATCTCTAAATGTCATCCTAATCAAAGGCAATGAAACTTTAAAAATTTAAAAAATTTTGCTAG
AGGTCTTGAAAATTGTGTCCAGAGGTCTTATAAGTTTT
Found at i:415207 original size:96 final size:95
Alignment explanation
Indices: 414989--415243 Score: 275
Period size: 96 Copynumber: 2.7 Consensus size: 95
414979 GTCTTACAAA
* * ** * * *
414989 TCTT-AAAATCTTTGAATGTTCCTCT-AATCAGAGGCATTGAAACTTT-AAAACTTAAAATGATT
1 TCTTAAAAATCTTTGAATGATCCT-TGTATCAGAGGTGTTGAAACTTTAAAAAATTAAAAGGTTT
* ** *
415051 TGTCGGAGGTCTTGAAAATTATGTTTGGAGG
65 TGCCGGAGGTCTTGAAAATTATGTCAGAAGG
* * * *
415082 TTTTAAAAATCTTTGAACGCTCCTCGTATCAGAGGTGTTGAAACTTTAAAAAATTAAAAGGTTTT
1 TCTTAAAAATCTTTGAATGATCCTTGTATCAGAGGTGTTGAAACTTTAAAAAATTAAAAGGTTTT
*
415147 GCCGGAAGTTCTT-AGAAATTATGTCAGAAGG
66 GCCGG-AGGTCTTGA-AAATTATGTCAGAAGG
* * *
415178 TCTTAAAAATCTTTGAATGATCCTTGTATCAAAGGTGTTGAAACTTTAAAGATTTAAAATGGTTT
1 TCTTAAAAATCTTTGAATGATCCTTGTATCAGAGGTGTTGAAACTTTAAAAAATTAAAA-GGTTT
415243 T
65 T
415244 CACCTAATCA
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
93 3 0.02
94 35 0.26
95 19 0.14
96 71 0.53
97 6 0.04
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (95 bp):
TCTTAAAAATCTTTGAATGATCCTTGTATCAGAGGTGTTGAAACTTTAAAAAATTAAAAGGTTTT
GCCGGAGGTCTTGAAAATTATGTCAGAAGG
Found at i:416251 original size:6 final size:6
Alignment explanation
Indices: 416236--416285 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
416226 TTCTTCTTTC
* *
416236 TTTTTA TTTTTG TTTTTG TTTTTG CTTTTTTG TTTTTTG TTTTTA TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG --TTTTTG -TTTTTG TTTTTG TTTTT
416286 TTAACTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 27 0.68
7 7 0.17
8 6 0.15
ACGTcount: A:0.04, C:0.02, G:0.10, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:416266 original size:21 final size:20
Alignment explanation
Indices: 416221--416286 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
416211 GTCCTCCTTC
* * *
416221 ATTTTTTCTTCTTTCTTTTT
1 ATTTTTTGTTTTTTGTTTTT
416241 A-TTTTTG-TTTTTGTTTTT
1 ATTTTTTGTTTTTTGTTTTT
*
416259 GCTTTTTTGTTTTTTGTTTTT
1 -ATTTTTTGTTTTTTGTTTTT
416280 ATTTTTT
1 ATTTTTT
416287 TAACTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.24
19 5 0.13
20 13 0.34
21 11 0.29
ACGTcount: A:0.05, C:0.06, G:0.08, T:0.82
Consensus pattern (20 bp):
ATTTTTTGTTTTTTGTTTTT
Done.